| fastqc |
20 |
- results/2018-10-03/fastqc/GM0h.html
- results/2018-10-03/fastqc/GM0h.zip
- results/2018-10-03/fastqc/GM30min.html
- results/2018-10-03/fastqc/GM30min.zip
- results/2018-10-03/fastqc/GM1h.html
- results/2018-10-03/fastqc/GM1h.zip
- results/2018-10-03/fastqc/GM2h.html
- results/2018-10-03/fastqc/GM2h.zip
- results/2018-10-03/fastqc/GM4h.html
- results/2018-10-03/fastqc/GM4h.zip
- results/2018-10-03/fastqc/GM6h.html
- results/2018-10-03/fastqc/GM6h.zip
- results/2018-10-03/fastqc/GM9h.html
- results/2018-10-03/fastqc/GM9h.zip
- results/2018-10-03/fastqc/GM12h.html
- results/2018-10-03/fastqc/GM12h.zip
- results/2018-10-03/fastqc/GM18h.html
- results/2018-10-03/fastqc/GM18h.zip
- results/2018-10-03/fastqc/GM24h.html
- results/2018-10-03/fastqc/GM24h.zip
- results/2018-10-03/fastqc/GM48h.html
- results/2018-10-03/fastqc/GM48h.zip
- results/2018-10-03/fastqc/GM72h.html
- results/2018-10-03/fastqc/GM72h.zip
- results/2018-10-03/fastqc/IMR0h.html
- results/2018-10-03/fastqc/IMR0h.zip
- results/2018-10-03/fastqc/IMR30min.html
- results/2018-10-03/fastqc/IMR30min.zip
- results/2018-10-03/fastqc/IMR1h.html
- results/2018-10-03/fastqc/IMR1h.zip
- results/2018-10-03/fastqc/IMR2h.html
- results/2018-10-03/fastqc/IMR2h.zip
- results/2018-10-03/fastqc/IMR4h.html
- results/2018-10-03/fastqc/IMR4h.zip
- results/2018-10-03/fastqc/IMR6h.html
- results/2018-10-03/fastqc/IMR6h.zip
- results/2018-10-03/fastqc/IMR12h.html
- results/2018-10-03/fastqc/IMR12h.zip
- results/2018-10-03/fastqc/IMR24h.html
- results/2018-10-03/fastqc/IMR24h.zip
|
|
|
| GM19_sample_pos2bed |
12 |
- results/2019-01-28/GM/GM0h_groseq_peak.bed
- results/2019-01-28/GM/GM30min_groseq_peak.bed
- results/2019-01-28/GM/GM1h_groseq_peak.bed
- results/2019-01-28/GM/GM2h_groseq_peak.bed
- results/2019-01-28/GM/GM4h_groseq_peak.bed
- results/2019-01-28/GM/GM6h_groseq_peak.bed
- results/2019-01-28/GM/GM9h_groseq_peak.bed
- results/2019-01-28/GM/GM12h_groseq_peak.bed
- results/2019-01-28/GM/GM18h_groseq_peak.bed
- results/2019-01-28/GM/GM24h_groseq_peak.bed
- results/2019-01-28/GM/GM48h_groseq_peak.bed
- results/2019-01-28/GM/GM72h_groseq_peak.bed
|
|
|
| IMR_sample_pos2bed |
8 |
- results/2019-01-28/IMR/IMR0h_groseq_peak.bed
- results/2019-01-28/IMR/IMR30min_groseq_peak.bed
- results/2019-01-28/IMR/IMR1h_groseq_peak.bed
- results/2019-01-28/IMR/IMR2h_groseq_peak.bed
- results/2019-01-28/IMR/IMR4h_groseq_peak.bed
- results/2019-01-28/IMR/IMR6h_groseq_peak.bed
- results/2019-01-28/IMR/IMR12h_groseq_peak.bed
- results/2019-01-28/IMR/IMR24h_groseq_peak.bed
|
|
|
| test_IMR_vs_Peng |
1 |
- results/2018-11-10/test/IMR_eRNA_vs_Peng.bed
|
|
|
| test_IMR_vs_GM19 |
1 |
- results/2018-11-10/test/IMR_eRNA_vs_GM19.bed
|
|
|
| test_IMR_vs_liftOver |
1 |
- results/2018-11-10/test/IMR_eRNA_vs_liftOver.bed
|
|
|
| genes_foldchange |
2 |
- results/2019-06-26/dge/foldchange/GM19_foldchange.tsv
- results/2019-06-26/dge/foldchange/IMR_foldchange.tsv
|
|
|
| eRNA_link_genes |
2 |
- results/2019-08-26/GM19_link_eRNA.bed
- results/2019-08-26/IMR_link_eRNA.bed
|
|
|
| eRNA_link_area |
1 |
- results/2019-08-26/eRNA_viral.bed
|
|
|
| GM19_eRNA_merge_counts |
1 |
- results/2019-06-03/eRNA/counts/GM19_merged.txt
|
|
|
| IMR_eRNA_merge_counts |
1 |
- results/2019-06-03/eRNA/counts/IMR_merged.txt
|
|
|
| eRNA_viral_foldchange |
2 |
- results/2019-09-27/de/foldchange/GM19_foldchange.tsv
- results/2019-09-27/de/foldchange/IMR_foldchange.tsv
|
|
|
| test_eRNA_check_L2 |
2 |
- results/2019-08-26/GM19_L2.bed
- results/2019-08-26/IMR_L2.bed
|
|
|
| test_homer_check_L2 |
2 |
- results/2019-10-01/GM19_genes_L2.bed
- results/2019-10-01/IMR_genes_L2.bed
|
|
|
| bed_check_L2 |
8 |
- results/2019-10-06/l2/IMR0h_bam_L2.bed
- results/2019-10-06/l2/IMR30min_bam_L2.bed
- results/2019-10-06/l2/IMR1h_bam_L2.bed
- results/2019-10-06/l2/IMR2h_bam_L2.bed
- results/2019-10-06/l2/IMR4h_bam_L2.bed
- results/2019-10-06/l2/IMR6h_bam_L2.bed
- results/2019-10-06/l2/IMR12h_bam_L2.bed
- results/2019-10-06/l2/IMR24h_bam_L2.bed
|
|
|
| test_report_L2 |
1 |
- results/2019-10-01/L2.tsv
|
|
|
| GM19_sample_findPeaks |
12 |
- results/2019-01-28/GM/GM0h_groseq_peak.gtf
- results/2019-01-28/GM/GM30min_groseq_peak.gtf
- results/2019-01-28/GM/GM1h_groseq_peak.gtf
- results/2019-01-28/GM/GM2h_groseq_peak.gtf
- results/2019-01-28/GM/GM4h_groseq_peak.gtf
- results/2019-01-28/GM/GM6h_groseq_peak.gtf
- results/2019-01-28/GM/GM9h_groseq_peak.gtf
- results/2019-01-28/GM/GM12h_groseq_peak.gtf
- results/2019-01-28/GM/GM18h_groseq_peak.gtf
- results/2019-01-28/GM/GM24h_groseq_peak.gtf
- results/2019-01-28/GM/GM48h_groseq_peak.gtf
- results/2019-01-28/GM/GM72h_groseq_peak.gtf
|
docker://emiller88/homer:latest |
|
| IMR_sample_findPeaks |
8 |
- results/2019-01-28/IMR/IMR0h_groseq_peak.gtf
- results/2019-01-28/IMR/IMR30min_groseq_peak.gtf
- results/2019-01-28/IMR/IMR1h_groseq_peak.gtf
- results/2019-01-28/IMR/IMR2h_groseq_peak.gtf
- results/2019-01-28/IMR/IMR4h_groseq_peak.gtf
- results/2019-01-28/IMR/IMR6h_groseq_peak.gtf
- results/2019-01-28/IMR/IMR12h_groseq_peak.gtf
- results/2019-01-28/IMR/IMR24h_groseq_peak.gtf
|
docker://emiller88/homer:latest |
|
| IMR_HistonesIntersect |
1 |
- results/2018-12-02/IMR_eRNA.bed
|
|
|
| GM_hg19_HistonesIntersect |
1 |
- results/2018-12-02/GM19_eRNA.bed
|
|
|
| GM18_sort_liftOver_Bed |
1 |
- results/2018-11-10/eRNA_GM_liftover_hg19.sorted.bed
|
|
|
| genes_tpm |
2 |
- results/2019-06-26/dge/tpm/GM19_tpm.txt
- results/2019-06-26/dge/tpm/IMR_tpm.txt
|
|
|
| genes_ripgrep_all |
2 |
- results/2019-06-26/dge/rg/GM19_de_genes.gtf
- results/2019-06-26/dge/rg/IMR_de_genes.gtf
|
|
|
| eRNA_link_merge |
1 |
- results/2019-08-26/eRNA_merged.bed
|
|
|
| eRNA_link_overlap |
1 |
- results/2019-08-26/eRNA_overlap_viral.bed
|
|
|
| GM19_eRNA_feature_counts |
12 |
- results/2019-06-03/eRNA/counts/per_sample/GM0h.txt
- results/2019-06-03/eRNA/qc/feature_counts/GM0h.txt
- results/2019-06-03/eRNA/counts/per_sample/GM30min.txt
- results/2019-06-03/eRNA/qc/feature_counts/GM30min.txt
- results/2019-06-03/eRNA/counts/per_sample/GM1h.txt
- results/2019-06-03/eRNA/qc/feature_counts/GM1h.txt
- results/2019-06-03/eRNA/counts/per_sample/GM2h.txt
- results/2019-06-03/eRNA/qc/feature_counts/GM2h.txt
- results/2019-06-03/eRNA/counts/per_sample/GM4h.txt
- results/2019-06-03/eRNA/qc/feature_counts/GM4h.txt
- results/2019-06-03/eRNA/counts/per_sample/GM6h.txt
- results/2019-06-03/eRNA/qc/feature_counts/GM6h.txt
- results/2019-06-03/eRNA/counts/per_sample/GM9h.txt
- results/2019-06-03/eRNA/qc/feature_counts/GM9h.txt
- results/2019-06-03/eRNA/counts/per_sample/GM12h.txt
- results/2019-06-03/eRNA/qc/feature_counts/GM12h.txt
- results/2019-06-03/eRNA/counts/per_sample/GM18h.txt
- results/2019-06-03/eRNA/qc/feature_counts/GM18h.txt
- results/2019-06-03/eRNA/counts/per_sample/GM24h.txt
- results/2019-06-03/eRNA/qc/feature_counts/GM24h.txt
- results/2019-06-03/eRNA/counts/per_sample/GM48h.txt
- results/2019-06-03/eRNA/qc/feature_counts/GM48h.txt
- results/2019-06-03/eRNA/counts/per_sample/GM72h.txt
- results/2019-06-03/eRNA/qc/feature_counts/GM72h.txt
|
|
|
| IMR_eRNA_feature_counts |
8 |
- results/2019-06-03/eRNA/counts/per_sample/IMR0h.txt
- results/2019-06-03/eRNA/qc/feature_counts/IMR0h.txt
- results/2019-06-03/eRNA/counts/per_sample/IMR30min.txt
- results/2019-06-03/eRNA/qc/feature_counts/IMR30min.txt
- results/2019-06-03/eRNA/counts/per_sample/IMR1h.txt
- results/2019-06-03/eRNA/qc/feature_counts/IMR1h.txt
- results/2019-06-03/eRNA/counts/per_sample/IMR2h.txt
- results/2019-06-03/eRNA/qc/feature_counts/IMR2h.txt
- results/2019-06-03/eRNA/counts/per_sample/IMR4h.txt
- results/2019-06-03/eRNA/qc/feature_counts/IMR4h.txt
- results/2019-06-03/eRNA/counts/per_sample/IMR6h.txt
- results/2019-06-03/eRNA/qc/feature_counts/IMR6h.txt
- results/2019-06-03/eRNA/counts/per_sample/IMR12h.txt
- results/2019-06-03/eRNA/qc/feature_counts/IMR12h.txt
- results/2019-06-03/eRNA/counts/per_sample/IMR24h.txt
- results/2019-06-03/eRNA/qc/feature_counts/IMR24h.txt
|
|
|
| eRNA_viral_tpm |
2 |
- results/2019-09-27/de/tpm/GM19_tpm.txt
- results/2019-09-27/de/tpm/IMR_tpm.txt
|
|
|
| homer_meta_pos2bed |
2 |
- results/2018-11-07/GM19_meta_groseq_peak.bed
- results/2018-11-07/IMR_meta_groseq_peak.bed
|
|
|
| IMR_bam_bed |
8 |
- results/2019-10-06/IMR/IMR0h.bed
- results/2019-10-06/IMR/IMR30min.bed
- results/2019-10-06/IMR/IMR1h.bed
- results/2019-10-06/IMR/IMR2h.bed
- results/2019-10-06/IMR/IMR4h.bed
- results/2019-10-06/IMR/IMR6h.bed
- results/2019-10-06/IMR/IMR12h.bed
- results/2019-10-06/IMR/IMR24h.bed
|
|
|
| GM19_sample_makeTagDirectory |
12 |
- results/2019-01-28/GM/GM0h_tagDir
- results/2019-01-28/GM/GM30min_tagDir
- results/2019-01-28/GM/GM1h_tagDir
- results/2019-01-28/GM/GM2h_tagDir
- results/2019-01-28/GM/GM4h_tagDir
- results/2019-01-28/GM/GM6h_tagDir
- results/2019-01-28/GM/GM9h_tagDir
- results/2019-01-28/GM/GM12h_tagDir
- results/2019-01-28/GM/GM18h_tagDir
- results/2019-01-28/GM/GM24h_tagDir
- results/2019-01-28/GM/GM48h_tagDir
- results/2019-01-28/GM/GM72h_tagDir
|
|
|
| unzip_hg19_uniqmap |
1 |
- data/2019-07-26/hg19-50nt-uniqmap
|
|
|
| IMR_sample_makeTagDirectory |
8 |
- results/2019-01-28/IMR/IMR0h_tagDir
- results/2019-01-28/IMR/IMR30min_tagDir
- results/2019-01-28/IMR/IMR1h_tagDir
- results/2019-01-28/IMR/IMR2h_tagDir
- results/2019-01-28/IMR/IMR4h_tagDir
- results/2019-01-28/IMR/IMR6h_tagDir
- results/2019-01-28/IMR/IMR12h_tagDir
- results/2019-01-28/IMR/IMR24h_tagDir
|
docker://emiller88/homer:latest |
|
| IMR_RemoveGenes |
1 |
- results/2018-11-09/IMR_groseq_noGenes.bed
|
|
|
| IMR_sort_Histones_Bed |
2 |
- data/2018-11-13/IMR/IMR_H3K27ac.sorted.bed
- data/2018-11-13/IMR/IMR_H3K4me1.sorted.bed
|
|
|
| GM19_RemoveGenes |
1 |
- results/2018-11-09/GM19_meta_groseq_noGenes.bed
|
|
|
| hg19_sort_Histones_Bed |
2 |
- data/2018-11-13/GM19/GM19_H3K27ac.sorted.bed
- data/2018-11-13/GM19/GM19_H3K4me1.sorted.bed
|
|
|
| GM18_liftOver_eRNAs |
1 |
- results/2018-11-10/eRNA_GM_liftover_hg19.bed
|
|
|
| GM19_merge_counts |
1 |
- results/2019-06-03/GM19/counts/merged.txt
|
|
|
| IMR_merge_counts |
1 |
- results/2019-06-03/IMR/counts/merged.txt
|
|
|
| refSeq |
2 |
- data/2018-11-09/hg19/genes.gtf
- data/2018-11-09/hg18/genes.gtf
|
|
|
| eRNA_saf_viral |
1 |
- results/2019-09-27/eRNA_viral.saf
|
|
|
| homer_meta_findPeaks |
2 |
- results/2018-11-07/GM19_meta_transcripts.txt
- results/2018-11-07/IMR_meta_transcripts.txt
|
docker://emiller88/homer:latest |
|
| download_hg19_uniqmap |
1 |
- data/2019-07-26/hg19uniqmap.zip
|
|
|
| hg19_fixBEDcoordinates |
1 |
- data/2018-11-09/hg19/hg19_slop_refseq.sorted.bed
|
|
|
| IMR_convert_Histones_to_Bed |
2 |
- data/2018-11-13/IMR/IMR_H3K27ac.bed
- data/2018-11-13/IMR/IMR_H3K4me1.bed
|
|
|
| hg19_convert_Histones_to_Bed |
2 |
- data/2018-11-13/GM19/GM19_H3K27ac.bed
- data/2018-11-13/GM19/GM19_H3K4me1.bed
|
|
|
| GM18_HistonesIntersect |
1 |
- results/2018-11-10/GM18_eRNA.bed
|
|
|
| download_mapChain |
1 |
- data/2018-11-10/hg18ToHg19.over.chain
|
docker://continuumio/miniconda3:4.6.14 |
|
| GM19_feature_counts |
11 |
- results/2019-06-03/GM19/counts/per_sample/GM0h.txt
- results/2019-06-03/GM19/qc/feature_counts/GM0h.txt
- results/2019-06-03/GM19/counts/per_sample/GM30min.txt
- results/2019-06-03/GM19/qc/feature_counts/GM30min.txt
- results/2019-06-03/GM19/counts/per_sample/GM1h.txt
- results/2019-06-03/GM19/qc/feature_counts/GM1h.txt
- results/2019-06-03/GM19/counts/per_sample/GM2h.txt
- results/2019-06-03/GM19/qc/feature_counts/GM2h.txt
- results/2019-06-03/GM19/counts/per_sample/GM4h.txt
- results/2019-06-03/GM19/qc/feature_counts/GM4h.txt
- results/2019-06-03/GM19/counts/per_sample/GM6h.txt
- results/2019-06-03/GM19/qc/feature_counts/GM6h.txt
- results/2019-06-03/GM19/counts/per_sample/GM9h.txt
- results/2019-06-03/GM19/qc/feature_counts/GM9h.txt
- results/2019-06-03/GM19/counts/per_sample/GM12h.txt
- results/2019-06-03/GM19/qc/feature_counts/GM12h.txt
- results/2019-06-03/GM19/counts/per_sample/GM18h.txt
- results/2019-06-03/GM19/qc/feature_counts/GM18h.txt
- results/2019-06-03/GM19/counts/per_sample/GM24h.txt
- results/2019-06-03/GM19/qc/feature_counts/GM24h.txt
- results/2019-06-03/GM19/counts/per_sample/GM48h.txt
- results/2019-06-03/GM19/qc/feature_counts/GM48h.txt
|
|
|
| IMR_feature_counts |
8 |
- results/2019-06-03/IMR/counts/per_sample/IMR0h.txt
- results/2019-06-03/IMR/qc/feature_counts/IMR0h.txt
- results/2019-06-03/IMR/counts/per_sample/IMR30min.txt
- results/2019-06-03/IMR/qc/feature_counts/IMR30min.txt
- results/2019-06-03/IMR/counts/per_sample/IMR1h.txt
- results/2019-06-03/IMR/qc/feature_counts/IMR1h.txt
- results/2019-06-03/IMR/counts/per_sample/IMR2h.txt
- results/2019-06-03/IMR/qc/feature_counts/IMR2h.txt
- results/2019-06-03/IMR/counts/per_sample/IMR4h.txt
- results/2019-06-03/IMR/qc/feature_counts/IMR4h.txt
- results/2019-06-03/IMR/counts/per_sample/IMR6h.txt
- results/2019-06-03/IMR/qc/feature_counts/IMR6h.txt
- results/2019-06-03/IMR/counts/per_sample/IMR12h.txt
- results/2019-06-03/IMR/qc/feature_counts/IMR12h.txt
- results/2019-06-03/IMR/counts/per_sample/IMR24h.txt
- results/2019-06-03/IMR/qc/feature_counts/IMR24h.txt
|
|
|
| GM19_meta_makeTagDirectory |
1 |
- results/2018-11-07/GM19_meta_tagDir
|
|
|
| IMR_meta_makeTagDirectory |
1 |
- results/2018-11-07/IMR_meta_tagDir
|
|
|
| hg19_slopRefSeq |
1 |
- data/2018-11-09/hg19/hg19_slop_refseq.bed
|
|
|
| IMR_alignHistones |
2 |
- data/2018-11-13/IMR/IMR_H3K27ac.bam
- data/2018-11-13/IMR/IMR_H3K4me1.bam
|
|
- bowtie2 ==2.3.2
- samtools ==1.5
|
| hg19_alignHistones |
2 |
- data/2018-11-13/GM19/GM19_H3K27ac.bam
- data/2018-11-13/GM19/GM19_H3K4me1.bam
|
|
- bowtie2 ==2.3.5
- samtools ==1.9
|
| hg18_RemoveGenes |
1 |
- results/2018-11-09/GM18_meta_groseq_noGenes.bed
|
|
|
| GM18_sort_Histones_Bed |
2 |
- data/2018-11-13/GM18/GM18_H3K27ac.sorted.bed
- data/2018-11-13/GM18/GM18_H3K4me1.sorted.bed
|
|
|
| refSeq_bed |
1 |
- data/2018-11-09/hg19/genes.bed
|
|
|
| hg19_UCSC_chrom_size |
1 |
- data/2019-09-25/hg19.chrom.sizes
|
|
|
| IMR_H3K27ac_fastq |
1 |
- data/2018-11-13/IMR_H3K27ac.fastq
|
docker://continuumio/miniconda3:4.6.14 |
|
| IMR_H3K4me1_fastq |
1 |
- data/2018-11-13/IMR_H3K4me1.fastq
|
docker://continuumio/miniconda3:4.6.14 |
|
| GM_H3K27ac_fastq |
1 |
- data/2018-11-13/GM_H3K27ac.fastq
|
|
|
| GM_H3K4me1_fastq |
1 |
- data/2018-11-13/GM_H3K4me1.fastq
|
|
|
| GM18_meta_pos2bed |
1 |
- results/2018-11-07/GM18_meta_groseq_peak.bed
|
|
|
| GM18_convert_Histones_to_Bed |
2 |
- data/2018-11-13/GM18/GM18_H3K27ac.bed
- data/2018-11-13/GM18/GM18_H3K4me1.bed
|
|
|
| GM18_meta_findPeaks |
1 |
- results/2018-11-07/GM18_meta_groseq_peak.gtf
|
docker://emiller88/homer:latest |
|
| GM18_alignHistones |
2 |
- data/2018-11-13/GM18/GM18_H3K27ac.bam
- data/2018-11-13/GM18/GM18_H3K4me1.bam
|
|
- bowtie2 ==2.3.5
- samtools ==1.9
|
| GM18_meta_makeTagDirectory |
1 |
- results/2018-11-07/GM18_meta_tagDir
|
docker://emiller88/homer:latest |
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